[maker-devel] Format error detected with maker2eval_gtf

[Zoe Clarke]

Hello!

I am currently working with an annotation from Maker that has just finished. Unfortunately I think there are some errors in my annotation, as a lot of my reads from a test RNA-seq alignment got discarded from my analysis. The analysis tool suggested my annotation might have overlapping reads.

I am trying to figure out what went wrong with my annotation, and the closest hint I have are error messages that I receive from running maker2eval_gtf on my output merged gff file. It appears every line of my gff is producing the following errors:

Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 244, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 245, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 246, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 35, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 37, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 38, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 39, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 40, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 41, <IN> line 200199481.

Do you know what issue this might indicate for my gff? At this point, I have done no filtering, just merged the files with gff3_merge.

Thank you so much, and please let me know if there is anything else I can provide to inform you more about my issue!

Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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